In river-floodplain ecosystems, overbank flows interact with floodplain geomorphology to generate a network of transient inter-waterbody connections. Heterogeneity in the characteristics of these connections may interact with species-specific dispersal capacity to affect the maintenance of diversity and community assembly on the floodplain. We modelled the immigration and emigration rates of nine species of fish entering and leaving a large floodplain lake during a hydrological connection with the parent river. Dispersal rates were modelled as a continuous function of time-since-connection over 3 months, with the aim of testing for species-specific patterns in (a) the timing and magnitudes of lateral dispersal, and (b) the balance between total immigration into, and emigration from, the lake. Significant interspecific variation in the timing and magnitude of lateral dispersal was evident. Magnitude of lateral dispersal was not a function of local abundance for all species. Further, the balance between immigration to, and emigration from, the lake varied significantly across species, and over time within species. The immigration–emigration balance of a species was not related to its magnitude of lateral dispersal, but may be related to its behavioural and life-history traits. Spatial heterogeneity in the duration of inter-waterbody connections may interact with species-specific dispersal functions to shape assembly of floodplain communities. Accordingly, habitat heterogeneity among floodplain waterbodies is not strictly necessary for heterogeneity in fish community composition. These dynamics have implications for the maintenance of diversity in river-floodplain fish metacommunities under both natural and managed connectivity regimes.